LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 2
  using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units        electron
dimension    3
boundary     p p p
atom_style   atomic
atom_modify  map yes
pair_style   none

# Time step (in femtoseconds)
timestep     0.5

# Temperature (in Kelvin)
variable     Temp equal 17.4

# Force constant (in Hartree energies per Bohr radius squared)
variable     k equal 1.2154614120000001e-08

# Number of beads
variable     Nbeads equal 4
variable     ibead uloop ${Nbeads} pad
variable     ibead uloop 4 pad
variable     seed equal 18889

# Create box and atoms. All distances are in Bohr
region       box block -1500 1500 -1500 1500 -1500 1500
create_box   1 box
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
  1 by 1 by 1 MPI processor grid
variable     a loop 3
label        loop
variable     x1 equal -15.0+0.5*v_a
variable     y1 equal 10.0-0.5*v_a
variable     z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14.5 ${y1} ${z1}
create_atoms 1 single -14.5 9.5 ${z1}
create_atoms 1 single -14.5 9.5 1.5
Created 1 atoms
  using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
  create_atoms CPU = 0.000 seconds
next         a
jump         SELF loop
variable     x1 equal -15.0+0.5*v_a
variable     y1 equal 10.0-0.5*v_a
variable     z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14 ${y1} ${z1}
create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2
Created 1 atoms
  using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
  create_atoms CPU = 0.000 seconds
next         a
jump         SELF loop
variable     x1 equal -15.0+0.5*v_a
variable     y1 equal 10.0-0.5*v_a
variable     z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -13.5 ${y1} ${z1}
create_atoms 1 single -13.5 8.5 ${z1}
create_atoms 1 single -13.5 8.5 2.5
Created 1 atoms
  using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
  create_atoms CPU = 0.000 seconds
next         a
jump         SELF loop

# Electron mass (in amu)
mass         1 0.00054858

# Initialize velocities
velocity     all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
velocity     all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
velocity     all create 17.4 18889${ibead} mom yes rot yes dist gaussian
velocity     all create 17.4 188893 mom yes rot yes dist gaussian

# Add harmonic external force
fix          harm all spring/self ${k}
fix          harm all spring/self 1.215461412e-08

# Add harmonic potential energy to total energy and potential energy
fix_modify   harm energy yes

# PIMD command
fix          pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
fix          pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no

# Outputs
variable prim_kinetic  equal f_pimdb[5]
variable virial        equal f_pimdb[6]

thermo_style custom step pe v_virial v_prim_kinetic
thermo          1

run             100
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
   Step         PotEng        v_virial    v_prim_kinetic
         0   0              1.3661449e-08  0.0009918329 
         1   8.3480048e-10  1.8742641e-09  0.00099182267
         2   2.8201389e-09  7.1801177e-09  0.00099180053
         3   7.3605781e-09  1.4372388e-08  0.00099176038
         4   1.4967393e-08  3.1274072e-08  0.00099170266
         5   2.4978087e-08  5.2470231e-08  0.00099162511
         6   3.5908849e-08  7.2301291e-08  0.00099153   
         7   4.8226614e-08  9.5440683e-08  0.00099141194
         8   6.3621045e-08  1.1669162e-07  0.00099127168
         9   8.0119736e-08  1.3551097e-07  0.00099109846
        10   9.7965614e-08  1.6050328e-07  0.00099089759
        11   1.1538858e-07  1.8645705e-07  0.0009906735 
        12   1.365443e-07   2.1181418e-07  0.00099042271
        13   1.5920175e-07  2.4218941e-07  0.00099012073
        14   1.8252589e-07  2.7507982e-07  0.00098977876
        15   2.0858909e-07  3.1771012e-07  0.00098940169
        16   2.3676046e-07  3.6075963e-07  0.00098900826
        17   2.689757e-07   4.0059005e-07  0.00098859985
        18   3.0022172e-07  4.3883585e-07  0.00098817535
        19   3.3127637e-07  4.8036287e-07  0.00098770764
        20   3.6044366e-07  5.2362451e-07  0.00098721266
        21   3.8484646e-07  5.7705077e-07  0.00098670407
        22   4.1435067e-07  6.3271105e-07  0.00098617081
        23   4.4508994e-07  6.9382916e-07  0.00098557406
        24   4.7879333e-07  7.5979853e-07  0.0009849612 
        25   5.0918223e-07  8.232213e-07   0.00098434971
        26   5.4733661e-07  8.9901705e-07  0.0009836645 
        27   5.7932115e-07  9.7033126e-07  0.0009830068 
        28   6.1775401e-07  1.0444697e-06  0.00098229311
        29   6.6883535e-07  1.1208219e-06  0.00098150213
        30   7.0943445e-07  1.1899315e-06  0.00098077686
        31   7.4477897e-07  1.2560026e-06  0.00098003518
        32   7.8183156e-07  1.3287355e-06  0.00097921099
        33   8.1987667e-07  1.399856e-06   0.0009784037 
        34   8.5514962e-07  1.4769272e-06  0.00097754491
        35   8.9607784e-07  1.5642459e-06  0.00097667479
        36   9.4986753e-07  1.6571388e-06  0.00097572641
        37   1.0024729e-06  1.7603492e-06  0.00097475881
        38   1.0526731e-06  1.8666516e-06  0.00097373763
        39   1.103419e-06   1.9696572e-06  0.0009727081 
        40   1.1640352e-06  2.0910539e-06  0.00097155807
        41   1.2292837e-06  2.2198868e-06  0.00097030871
        42   1.3024454e-06  2.3576614e-06  0.00096896762
        43   1.3788736e-06  2.496284e-06   0.00096760456
        44   1.4503248e-06  2.637657e-06   0.00096619083
        45   1.5334106e-06  2.795845e-06   0.00096470693
        46   1.6246777e-06  2.9727162e-06  0.00096303835
        47   1.715884e-06   3.1451673e-06  0.00096140406
        48   1.8096683e-06  3.3241907e-06  0.00095971129
        49   1.916714e-06   3.5094834e-06  0.00095790964
        50   2.0374848e-06  3.7049195e-06  0.00095603039
        51   2.1747488e-06  3.9139587e-06  0.0009540918 
        52   2.3236882e-06  4.1289537e-06  0.0009520767 
        53   2.4790586e-06  4.3481079e-06  0.00095003676
        54   2.6478101e-06  4.5702968e-06  0.00094802906
        55   2.8275135e-06  4.7928135e-06  0.00094600351
        56   3.0338638e-06  5.0253448e-06  0.0009438419 
        57   3.2428318e-06  5.2569331e-06  0.00094169256
        58   3.4414566e-06  5.4997767e-06  0.00093948055
        59   3.6324968e-06  5.7547729e-06  0.00093714003
        60   3.8269172e-06  6.0074589e-06  0.00093480857
        61   4.0183315e-06  6.2647899e-06  0.00093244785
        62   4.2263009e-06  6.5384938e-06  0.00092998209
        63   4.4382735e-06  6.8124372e-06  0.00092751453
        64   4.6488232e-06  7.0913777e-06  0.00092505171
        65   4.8707403e-06  7.3773956e-06  0.00092256944
        66   5.1178339e-06  7.6811232e-06  0.00091984092
        67   5.377713e-06   7.9951107e-06  0.0009170037 
        68   5.63843e-06    8.3096758e-06  0.00091414977
        69   5.8975743e-06  8.6232285e-06  0.00091137219
        70   6.168921e-06   8.9388929e-06  0.00090857909
        71   6.4488238e-06  9.2524846e-06  0.00090583473
        72   6.7115203e-06  9.5688611e-06  0.00090308342
        73   6.995134e-06   9.8873586e-06  0.00090026584
        74   7.284199e-06   1.0203245e-05  0.00089755256
        75   7.6029528e-06  1.0523755e-05  0.00089485804
        76   7.9431391e-06  1.0848398e-05  0.00089217189
        77   8.2768015e-06  1.1164286e-05  0.00088956967
        78   8.6058917e-06  1.1466652e-05  0.00088700311
        79   8.9683477e-06  1.177381e-05   0.00088439373
        80   9.3324487e-06  1.2059606e-05  0.00088199635
        81   9.6876036e-06  1.233837e-05   0.0008797438 
        82   1.0061754e-05  1.261531e-05   0.00087745162
        83   1.0457019e-05  1.2899972e-05  0.00087506863
        84   1.0866064e-05  1.3160246e-05  0.00087288444
        85   1.1298832e-05  1.3438712e-05  0.00087052617
        86   1.1762526e-05  1.372546e-05   0.00086818634
        87   1.2264941e-05  1.4017631e-05  0.00086572407
        88   1.2784125e-05  1.4328439e-05  0.000862992  
        89   1.332533e-05   1.4640964e-05  0.00086017364
        90   1.3897966e-05  1.4978644e-05  0.0008570595 
        91   1.4473024e-05  1.5307214e-05  0.00085411601
        92   1.5067033e-05  1.5649328e-05  0.00085112325
        93   1.5677943e-05  1.6015833e-05  0.0008479391 
        94   1.6254294e-05  1.6393131e-05  0.00084474237
        95   1.6791089e-05  1.674573e-05   0.00084165639
        96   1.7362795e-05  1.7094435e-05  0.00083858996
        97   1.7961498e-05  1.7451741e-05  0.00083536142
        98   1.8568337e-05  1.780703e-05   0.00083221292
        99   1.9188379e-05  1.8141862e-05  0.00082913227
       100   1.9789011e-05  1.8457846e-05  0.00082619877
Loop time of 0.00116163 on 1 procs for 100 steps with 3 atoms

Performance: 3718915419.639 fs/day, 0.000 hours/fs, 86086.005 timesteps/s, 258.258 katom-step/s
89.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 1.582e-06  | 1.582e-06  | 1.582e-06  |   0.0 |  0.14
Comm    | 1.3306e-05 | 1.3306e-05 | 1.3306e-05 |   0.0 |  1.15
Output  | 0.00017996 | 0.00017996 | 0.00017996 |   0.0 | 15.49
Modify  | 0.00090771 | 0.00090771 | 0.00090771 |   0.0 | 78.14
Other   |            | 5.907e-05  |            |       |  5.09

Nlocal:              3 ave           3 max           3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 41
Dangerous builds = 0
Total wall time: 0:00:00
